Hi Fish, this indicates that the parser choked on the alignment file. Could you send it to my address (i.e. not to the mailing list)? Normally, there is something wrong with the header portion, so it is OK if you just leave the header and the lines you sent along with your first email. Thanks, Gabor On Apr 25 2012, Zhang yu wrote:

Dear Gabor,

The error message shows nothing but part of the alignment file. I tried both Phenix 1.7.3 and 1.7.1.

Thanks, Fish

2012/4/25 Gabor Bunkoczi

...

Dear Fish,

can you let me know what the error message is and which Phenix version are you using? Your alignment file looks OK to me.

Thanks, Gabor

On Apr 25 2012, Zhang yu wrote:

Dear Phenixer,

...

When I used Sculptor to generate a new model, there is a error which I can not figure out. I input a PDB file (*.pdb) and an alignment file (*.aln).

The following is the log file (contents in ######). There seems something wrong with the *.aln file. ################# Reading PDB file ----------------

File name: **/**/******/******/**.pdb Separating solvent from macromolecules...

Reading alignment files -----------------------

1. **/**/**.aln

#####################

The following is the content of the alignment file:

**_** MVYSYTEKKRIRKDFGKRPQVLDVPYLLSI**QLDSFQKFIEQDPEGQY----GLEAAFRSV **_** ---------**MEIKRFGRIREVIPLPPLTEIQVESYRRAL** QADVPPEKRENVGIQAAFRET * **: :*: :* * .**::*::: :: * : *::****..

What is the problem with the alignment file?

Thank you in advance! Fish

-- ##############################**####################

Dr Gabor Bunkoczi

Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##############################**####################

______________________________**_________________ phenixbb mailing list [email protected] http://phenix-online.org/**mailman/listinfo/phenixbbhttp://phenix-online.org/mailman/listinfo/phenixbb

Hi Gabor, It works now. Thank you for your suggestion! Fish 2012/4/26 Gabor Bunkoczi

Hi Fish,

your line endings cause trouble. I assume you are running sculptor on either linux or mac, but your line endings are from windows (dos). I will change the parser so that it is independent of line endings. In the meantime, you can use the dos2unix utility to convert the linebreaks, and go ahead with your calculation.

Thanks for your help, Gabor

On Apr 25 2012, Zhang yu wrote:

Dear Gabor,

...

The error message shows nothing but part of the alignment file. I tried both Phenix 1.7.3 and 1.7.1.

Thanks, Fish

2012/4/25 Gabor Bunkoczi

Dear Fish,

...

can you let me know what the error message is and which Phenix version are you using? Your alignment file looks OK to me.

Thanks, Gabor

On Apr 25 2012, Zhang yu wrote:

Dear Phenixer,

...

When I used Sculptor to generate a new model, there is a error which I can not figure out. I input a PDB file (*.pdb) and an alignment file (*.aln).

The following is the log file (contents in ######). There seems something wrong with the *.aln file. ################# Reading PDB file ----------------

File name: **/**/******/******/**.pdb Separating solvent from macromolecules...

Reading alignment files -----------------------

1. **/**/**.aln

#####################

The following is the content of the alignment file:

**_** MVYSYTEKKRIRKDFGKRPQVLDVPYLLSI****QLDSFQKFIEQDPEGQY----**GLEAAFRSV **_** ---------****MEIKRFGRIREVIPLPPLTEIQVESYRRAL**** QADVPPEKRENVGIQAAFRET

* **: :*: :* * .**::*::: :: * : *::****..

What is the problem with the alignment file?

Thank you in advance! Fish

--

##############################****####################

Dr Gabor Bunkoczi

Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##############################****####################

______________________________****_________________ phenixbb mailing list [email protected] http://phenix-online.org/**** mailman/listinfo/phenixbbhttp://phenix-online.org/**mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb

...

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